3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling

A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.     

Correlations between adhesion hysteresis and friction at molecular scales

Correlations between adhesion hysteresis and local friction are theoretically and experimentally investigated. The model is based on the classical theory of adhesional friction, contact mechanics, capillary hysteresis, and nanoscale roughness. Adhesion hysteresis was found to scale with friction through the scaling factor containing a varying ratio of adhesion energy over the reduced Young's modulus. Capillary forces can offset the relationship between adhesion hysteresis and friction. Measurements on a wide range of engineering samples with varying adhesive and elastic properties confirm the model. Adhesion hysteresis is investigated under controlled, low humidity atmosphere via ultrasonic force microscopy. Friction is measured by the friction force microscopy.     

Micrometer scale adhesion on nanometer-scale patchy surfaces: adhesion rates, adhesion thresholds, and curvature-based selectivity

Using a model system based on electrostatics, we probe interactions between spherical particles (negative silica) and planar surfaces that present randomly placed discrete attractive regions, 10 nm in size, in a repulsive background (silica flats carrying cationic surface constructs). Experiments measure the adhesion rates of particles onto the patchy collecting surfaces from flowing dispersions, as a function of the surface loading of the attractive patches, for different particle sizes (0.5 and 1 mum diameter spheres) and different ionic strengths. Surfaces densely populated with patches, such that they present net electrostatic attractions to approaching particles, capture particles at the transport-limited (maximum) rate. Surfaces sparsely loaded with attractive patches (which present a repulsive mean field to approaching particles) are usually still adhesive, but the particle adhesion rate depends on particle size, ionic strength, and patch loading. Most significant is an adhesion threshold, a critical density of patches needed to capture particles. This threshold, which occurs at average patch spacings of 30 nm and larger and which can be tuned through ionic strength, comprises the ability of the patchy surfaces to selectively distinguish particles of different sizes or objects of different local curvature or roughness. The observation of such an adhesion threshold implicates spatial fluctuations in patch arrangement. In addition to experiments, this paper develops arguments for lengthscales that govern adhesion rate behavior, comparing particle geometry and fluctuation lengthscales, and then demonstrating qualitative consistency with the localized colloidal potentials involved.     

Interplay between hydrogen bond formation and multicenter pi-electron delocalization: intermolecular hydrogen bonds

The interplay between aromatic electron delocalization and intermolecular hydrogen bonding is thoroughly investigated using multicenter delocalization analysis. The effect on the hydrogen bond strength of aromatic electron delocalization within the acceptor and donor molecules is determined by means of the interaction energies between monomers, calculated at the B3LYP/6-311++G(d,p) level of theory. This magnitude is compared to variations of multicenter electron delocalization indices and covalent hydrogen bond indices, which are shown to correlate perfectly with the relative values of the interaction energies for the different complexes studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. All the hydrogen bonds are formed with oxygen as the acceptor atom; however, the atom bonded to the donor hydrogen has been either oxygen or nitrogen. The water-water complex is taken as reference, where the donor and acceptor molecular environments are modified by substituting the hydrogens and the hydroxyl group by phenol, furan, and pyrrole aromatic rings. The results here shown match perfectly with the qualitative expectations derived from the resonance model.     

Mechanism of adhesion between polymer fibers at nanoscale contacts

Adhesive force exists between polymer nano/microfibers. An elaborate experiment was performed to investigate the adhesion between polymer nano/microfibers using a nanoforce tensile tester. Electrospun polycaprolactone (PCL) fibers with diameters ranging from 0.4-2.2 μm were studied. The response of surface property of electrospun fiber to the environmental conditions was tracked by FTIR and atomic force microscopy (AFM) measurements. The effect of temperature on molecular orientation was examined by wide angle X-ray diffraction (WAXD). The adhesive force was found to increase with temperature and pull-off speed but insensitive to the change of relative humidity, and the abrupt increase of adhesion energy with temperature accompanied by a reduced molecular orientation in the amorphous part of fiber was observed. Results show that adhesion is mainly driven by van der Waals interactions between interdiffusion chain segments across the interface.     

Molecular simulation studies of nanoscale friction between phosphorylcholine self-assembled monolayer surfaces: correlation between surface hydration and friction

We performed all-atom molecular dynamics simulations to study the friction between surfaces covered with two phosphorylcholine self-assembled monolayers (PC-SAM) under shear. PC-SAM surfaces with a sqrt7 X sqrt7R19 degrees lattice structure and a parallel arrangement of the head groups were used as model zwitterionic surfaces. They provide a full representation of the zwitterionic nature of phospholipid surfaces, which are believed to play an important role in the lubrication of biological joints such as knees and hips. The surfaces were immersed in aqueous solutions and kept in contact with two regions of bulk water. Sodium chloride and potassium chloride solutions at various concentrations were employed to study the effects of the presence of ions on friction. The results show a strong relationship between surface hydration and friction. Higher ionic concentrations or ions with shorter Debye lengths cause a larger disruption to the hydration around the zwitterionic surfaces, leading to larger friction forces. In addition, the results show that under nanoscale confinement, the friction coefficients of PC-SAM surfaces in pure water are directly proportional to both shear velocity and surface separation distance. These results are comparable to previously published experimental studies.     

A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

Sliding friction between polymer surfaces: a molecular interpretation

For two contacting rigid bodies, the friction force F is proportional to the normal load and independent of the macroscopic contact area and relative velocity V (Amonton's law). With two mutually sliding polymer samples, the surface irregularities transmit deformation to the underlying material. Energy loss along the deformation cycles is responsible for the friction force, which now appears to depend strongly on V [see, e.g., N. Maeda et al., Science 297, 379 (2002)]. We base our theoretical interpretation on the assumption that polymer chains are mainly subjected to oscillatory "reptation" along their "tubes." At high deformation frequencies-i.e., with a large sliding velocity V-the internal viscosity due to the rotational energy barriers around chain bonds hinders intramolecular mobility. As a result, energy dissipation and the correlated friction force strongly diminish at large V. Derived from a linear differential equation for chain dynamics, our results are basically consistent with the experimental data by Maeda et al. [Science 297, 379 (2002)] on modified polystyrene. Although the bulk polymer is below T(g), we regard the first few chain layers below the surface to be in the liquid state. In particular, the observed maximum of F vs V is consistent with physically reasonable values of the molecular parameters. As a general result, the ratio FV is a steadily decreasing function of V, tending to V(-2) for large velocities. We evaluate a much smaller friction for a cross-linked polymer under the assumption that the junctions are effectively immobile, also in agreement with the experimental results of Maeda et al. [Science 297, 379 (2002)].     

Polypeptide friction and adhesion on hydrophobic and hydrophilic surfaces: a molecular dynamics case study

Using all-atomistic MD simulations including explicit water, the mobility and adhesion of a mildly hydrophobic single polypeptide chain adsorbed on hydrophobic and hydrophilic diamond surfaces is investigated by application of lateral and vertical pulling forces. Forced motion on the hydrophilic surface exhibits stick-slip due to breaking and reformation of hydrogen bonds; in contrast, on the hydrophobic surface, the motion is smooth. By carefully tuning the driving force magnitude, the linear-response regime is reached on a hydrophobic surface and equilibrium values for mobility and adhesive strength are obtained. On the hydrophilic surface, on the other hand, slow hydrogen-bond kinetics prevents equilibration and only upper bounds for adhesion force and mobility can be estimated. Whereas the desorption force is rather comparable on the two surfaces and differs at most by a factor of 2, the mobility on the hydrophilic surface is at least 30-fold reduced compared to the hydrophobic one. A simple model based on a single particle diffusing in a corrugated potential landscape suggests that cooperativity is rather limited and that the small mobility on a hydrophilic surface can be rationalized in terms of incoherently moving monomers. The experimentally well-known peptide mobility in bulk water is quantitatively reproduced in our simulations, which serves as a sensitive test on our methodology employed.     

Stick slip contact mechanics between dissimilar materials: effect of charging and large friction

Measurements of the contact radius as a function of applied force between a mica surface and a silica surface (mica/silica) in air are reported. The load/unload results show that the contact radius generally increases with applied force. Because of the presence of charging due to contact electrification, both a short-range van der Waals adhesion force and longer-range electrostatic adhesive interaction contribute to the measured force. The results indicate that approximately 20% of the pull-off force is due to van der Waals forces. The contact radius versus applied force results can be fit to Johnson-Kendall-Roberts (JKR) theory by considering that only the short-range van der Waals forces contribute to the work of adhesion and subtracting a constant longer-range electrostatic force. Also, an additional and unexpected step function is superimposed on the contact radius versus applied force curve. Thus, the contact diameter increases in a stepped dependence with increasing force. The stepped contact behavior is seen only for increasing force and is not observed when symmetric mica/mica or silica/silica contacts are measured. In humid conditions, the contact diameter of the mica/silica contact increases monotonically with applied force. Friction forces between the surfaces are also measured and the shear stress of a mica/silica interface is 100 times greater than the shear stress of a mica/mica interface. This large shear stress retards the increase in contact area as the force is increased and leads to the observed stepped contact mechanics behavior.     

Estimation of intramolecular hydrogen bond energy via molecular tailoring approach

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H...O bond energy is directly estimated by addition/subtraction of the single point individual fragment energies. This method is tested on polyhydroxy molecules at MP2 and B3LYP levels of theory. It is seen to be able to distinguish between weak ( approximately 1 kcal mol(-1)) and moderately strong ( approximately 5 kcal mol(-1)) hydrogen bonds in polyhydroxy molecules.     

氢键对分子器件电学特性的影响

利用密度泛函理论和弹性散射格林函数方法,研究了被不同官能团取代后的联苯分子的电输运特性.计算结果表明,由于氢键的影响,使得分子的电子结构发生了变化,特别是对电子在分子结内的跃迁几率影响较大,从而直接影响了分子器件的伏安特性.     

Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics

We report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.     

High-pressure studies of the hydrogen bond networks in molecular crystals

This article gives some examples of using high-pressure techniques to study hydrogen bond networks in molecular crystals.     

Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects

On the basis of recently synthesized calix[4]hydroquinone (CHQ) nanotubes which were self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (SHB), we have investigated the nature of 1-D SHB using first-principles calculations for all the systems including the solvent water. The H-bonds relay (i.e., contiguous H-bonds) effect in CHQs shortens the H...O bond distances significantly (by more than 0.2 A) and increases the bond dissociation energy to a large extent (by more than approximately 4 kcal/mol) due to the highly enhanced polarization effect along the H-bond relay chain. The H-bonds relay effect shows a large increase in the chemical shift associated with the SHB. The average binding energies for the infinite 1-D H-bond arrays of dioles and dions increase by approximately 4 and approximately 9 kcal/mol per H-bond, respectively. The solvent effect (due to nonbridging water molecules) has been studied by explicitly adding water molecules in the CHQ tube crystals. This effect is found to be small with slight weakening of the SHB strength; the H...O bond distance increases only by 0.02 A, and the average binding energy decreases by approximately 1 kcal/mol per H-bond. All these results based on the first-principles calculations are the first detailed analysis of energy gain by SHB and energy loss by solvent effect, based on a partitioning scheme of the interaction energy components. These reliable results elucidate not only the self-assembly phenomena based on the H-bond relay but also the solvent effect on the SHB strength.     

Inelastic collisions of molecular hydrogen: a comparison of results from quantum and classical mechanics

Full-dimensional quantum and classical calculations have been carried out for inelastic (nonreactive) energy transfer in H2+H2 on the ab initio potential energy surface of Boothroyd et al. [J. Chem. Phys. 116, 666 (2002)]. State-to-state cross sections are determined and compared for transitions from H2(0,j(ab))+H2(1,j(cd)). While there is excellent agreement for transitions involving small Deltaj, for larger Deltaj and for vibrational relaxation, significant differences are observed which exhibit no systematic trends. Reasons for this disagreement are discussed.     

Quantitative relationships between bond lengths,stretching vibrational frequencies,bond force constants,and bond orders in the hydrogen-bonded complexes involving hydrogen halides

To uncover the correlation between the bond length change and the corresponding stretching frequency shift of the proton donor D–H upon hydrogen bond formation, a series of hydrogen-bonded complexes involving HF and HCl which exhibit the characteristics of red-shifted hydrogen bond were investigated at the MP2/aug-cc-pVTZ, M062X/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ(GD3) levels of theory with CP optimizations. A statistical analysis of these complexes leads to the quantitative illustrations of the relations between bond length and stretching vibrational frequency, between bond length and bond force constant, between stretching vibrational frequency and bond force constant, between bond length and bond order for hydrohalides in a mathematical way, which would provide valuable insights into the explanation of the geometrical and spectroscopic behaviors during hydrogen bond formation.     

Proton affinity correlations between hydrogen and dihydrogen bond acceptors

Several series of hydrogen- and dihydrogen-bonded complexes with HCN, C2H2, HF, H2O, CH3CONH2, and CH3COOH as donors and H2O, MeOH, EtOH, MeOMe, NH3, NH2Me, NHMe2, NMe3, NEtMe2, and BH3-NMe3 as acceptors were investigated using the MP2/6-311++G(d,p) level of theory. The total lowering of the X-H stretching frequencies in the hydrogen-bonded complexes were linearly correlated with the proton affinities of the accepting bases. From comparison of hydrogen- and dihydrogen-bonded complexes, a scaling factor to estimate the exact proton affinity of a dihydrogen bond acceptor was developed. Further, the scaling factor involving linear donors (1.204) is marginally higher than that involving nonlinear donor molecules (1.162). Finally, it was found that, given identical conditions, a hydrogen bond will be about 16-20% stronger than a corresponding dihydrogen bond.     

Proton and deuterium NMR of hydrogen bonds: Relationship between isotope effects and the hydrogen bond potential

The difference in chemical shift between hydrogen bonded protons and deuterons has been examined both theoretically and experimentally. It is shown that valuable information about the hydrogen bond potential can be extracted from this isotope effect on chemical shifts.